UF Carpentries Workshop: Intro to Data Analysis with R and Version Control

November 4-5, 2019

9:00 AM - 4:30 PM

Instructors: Eve Bohnett, Dimitri Bourilkov, Chandra Earl, Geraldine Klarenberg, Brian Stucky

Helpers: Vratika Chaudhary, Jana Hilsenroth, Amy Kendig, Elise Morrison, Jennica Poongavanan, Ben Toh

General Information

The Carpentries aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including data management, basic R programming, data visualization, and version control. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 432 Newell Dr, Gainesville, FL 32603. Get directions with OpenStreetMap or Google Maps.

When: November 4-5, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). You should have permission to install software on your laptop. Before the workshop, please make sure that your laptop has a few specific software packages installed.

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can make learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will do our best to help.

Contact: Please email chaudharyv@ufl.edu , emorrison@ufl.edu or stuckyb@flmnh.ufl.edu for more information.


Registration

Space is limited to 24 participants for this workshop and registration is required. A fee of $46.00 will be charged and lunch will be provided on both days. Please plan on attending the entire time for both days.

Register for this workshop!

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

Before Pre-workshop survey
9:00 AM Data management with spreadsheets
10:30 Morning break
10:45 Using the Unix shell
12:00 PM Lunch break
1:00 Introduction to R
2:30 Afternoon break
2:45 Introduction to R, continued
4:30 END

Day 2

9:00 AM Version control with git
10:30 Morning break
10:45 Version control with git, continued
12:00 PM Lunch break
1:00 R: Data manipulation and visualization
2:30 Afternoon break
2:45 R data manipulation and visualization, continued
4:30 Post-workshop Survey
16:40 END

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Spreadsheet software

For this workshop, just about any spreadsheet software should work. We recommend LibreOffice, which is free, comes with feature-rich spreadsheet software, runs on all major operating systems, and is easy to install.

The Bash shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
    3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.